Query psy548
Match_columns 84
No_of_seqs 103 out of 364
Neff 4.6
Searched_HMMs 29240
Date Fri Aug 16 18:36:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy548.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/548hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1qkl_A RPB6, DNA-directed RNA 100.0 1.9E-37 6.3E-42 214.2 8.6 82 2-83 46-127 (127)
2 1twf_F ABC23, DNA-directed RNA 100.0 2.2E-36 7.4E-41 214.5 10.7 82 2-83 74-155 (155)
3 3h0g_F DNA-directed RNA polyme 100.0 1.1E-36 3.6E-41 213.5 8.4 79 2-80 64-142 (142)
4 4ayb_K DNA-directed RNA polyme 100.0 1.2E-30 4.1E-35 172.8 9.2 68 11-78 25-94 (95)
5 3lu0_E DNA-directed RNA polyme 99.6 1.1E-15 3.9E-20 100.0 2.8 53 14-67 15-68 (91)
6 2a6h_E RNA polymerase omega ch 99.5 3.3E-14 1.1E-18 93.9 5.6 48 14-61 15-76 (99)
7 3hie_A Protein PSL1, exocyst c 57.2 8.1 0.00028 27.2 2.9 29 56-84 79-110 (171)
8 3a58_A Exocyst complex compone 36.0 18 0.0006 28.0 2.0 28 56-83 149-179 (320)
9 2kxh_B Peptide of FAR upstream 29.9 26 0.00089 18.4 1.5 9 22-30 13-21 (31)
10 2npt_A Dual specificity mitoge 29.1 45 0.0015 21.8 2.8 20 58-77 13-32 (106)
11 1jb0_D Photosystem 1 reaction 24.8 69 0.0023 21.9 3.2 26 53-78 72-98 (138)
No 1
>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} SCOP: a.143.1.2
Probab=100.00 E-value=1.9e-37 Score=214.23 Aligned_cols=82 Identities=79% Similarity=1.176 Sum_probs=79.1
Q ss_pred CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548 2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI 81 (84)
Q Consensus 2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~ 81 (84)
+|.++|+|+|||||||+||++|+||+||++||+|||+.++.+||++||++||++|+||++|+|++|||+||+|+++||.+
T Consensus 46 ~~~~~r~t~p~lTRYElARIiG~RAlQLs~GAppLVd~e~~~dPl~IAl~ElaeGkIpi~VrR~lPdg~yEd~~~~eL~i 125 (127)
T 1qkl_A 46 QANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELII 125 (127)
T ss_dssp TTCCCSSCCSSCCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCEEEEEEETTTEEEEESSSSSCS
T ss_pred CCccccccCCCcCHHHHHHHHHHHHHHHhcCCcceEcCCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeehhheec
Confidence 68899999999999999999999999999999999999877899999999999999999999999999999999999998
Q ss_pred ec
Q psy548 82 ID 83 (84)
Q Consensus 82 ~~ 83 (84)
.|
T Consensus 126 ~~ 127 (127)
T 1qkl_A 126 TD 127 (127)
T ss_dssp CC
T ss_pred cC
Confidence 65
No 2
>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F 1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F* 1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F 1y77_F* ...
Probab=100.00 E-value=2.2e-36 Score=214.46 Aligned_cols=82 Identities=60% Similarity=0.965 Sum_probs=79.1
Q ss_pred CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccce
Q psy548 2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELKI 81 (84)
Q Consensus 2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~~ 81 (84)
+|..+|+|++||||||+||++|+||+||++||+|||+.++.+||++||++||++|+||++|+|++|||+||+|+++||++
T Consensus 74 ~~~~~r~t~p~lTRYElARIiG~RAlQLsmGAppLVd~e~~~dPl~IAl~ElaeGkIPl~IrR~lPdG~yEd~~v~eL~~ 153 (155)
T 1twf_F 74 IPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV 153 (155)
T ss_dssp CCSSSCCSCSBCCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCEEEEEECTTSCEEEEETTTSBC
T ss_pred CCcccccCCCCcCHHHHHHHHHHHHHHHhcCCCcEEecCCCCCHHHHHHHHHHcCCCCeEEEEECCCCCEEEeeHHHhcc
Confidence 68899999999999999999999999999999999999877899999999999999999999999999999999999998
Q ss_pred ec
Q psy548 82 ID 83 (84)
Q Consensus 82 ~~ 83 (84)
.|
T Consensus 154 ~~ 155 (155)
T 1twf_F 154 DL 155 (155)
T ss_dssp CC
T ss_pred CC
Confidence 64
No 3
>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=1.1e-36 Score=213.48 Aligned_cols=79 Identities=65% Similarity=1.035 Sum_probs=76.8
Q ss_pred CCCCCcccCCCccHHHHHHHHHHHHHHHhcCCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccccc
Q psy548 2 VFSPSFIITIVIKRYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDELK 80 (84)
Q Consensus 2 ~~~~~r~t~~~ltrYelari~g~RArQL~~GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~el~ 80 (84)
+|.++|+|+|||||||+||++|+||+||++||||||+.++++||++||++||++|+|||+|+|++|||+||+|+++||.
T Consensus 64 ~~~~~R~T~pylTRYElARIiG~RAlQIsmGAp~LVd~~~~tdPl~IA~~EL~egkIPiiVrR~lPdgkyEdw~l~EL~ 142 (142)
T 3h0g_F 64 VAKEDRTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYLPDGSYEDWSVAELI 142 (142)
T ss_dssp CCTTSCCSCSSCCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCCEEECCCSSSCCCEEETTTCC
T ss_pred CCcccccCCCccCHHHHHHHHHHHHHHHHCCCCceEcCCCCCCHHHHHHHHHHcCCCceEEEEECCCCCEEEeEHHHcC
Confidence 6899999999999999999999999999999999999987899999999999999999999999999999999999984
No 4
>4ayb_K DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_I 4b1o_K 4b1p_I 2waq_K 2wb1_I 2pmz_K 3hkz_K
Probab=99.97 E-value=1.2e-30 Score=172.84 Aligned_cols=68 Identities=40% Similarity=0.618 Sum_probs=64.4
Q ss_pred CCccHHHHHHHHHHHHHHHhcCCCceeeCC--CCCChHHHHHHHHHcCCCCeEEEEecCCCcEEEeeccc
Q psy548 11 IVIKRYERARVLGTRALQIAMCAPVMVELE--GETDPLQIAMKELKARKIPIIIRRYLPDNSYEDWGIDE 78 (84)
Q Consensus 11 ~~ltrYelari~g~RArQL~~GA~plV~~~--~~~kp~~IAl~Ei~~gkI~~~i~R~~p~~~~e~~~l~e 78 (84)
+.|||||+||++|.||+||++||+|+|+++ +..||+.||.+|+.+|+|||+|+|++|||+||+|+|+|
T Consensus 25 ~kLTKYEkaRIiG~RA~Qis~GA~~~I~~~~~~~~Dp~~IA~~EL~~~kiP~iIrR~lPnG~~E~~~l~e 94 (95)
T 4ayb_K 25 NKLTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNGKIILLSLRK 94 (95)
T ss_dssp SSCCHHHHHHHHHHHHHHHHTCCCCSSCTTTSCSSCTHHHHHHHHHTTCCCEEEEEECTTSCEEEECCCC
T ss_pred ccccHHHHHHHHHHHHHHHHCCCCceEeCCCCCCCCHHHHHHHHHHcCCCCEEEEEeCCCCCEEEEEecc
Confidence 449999999999999999999999999986 36899999999999999999999999999999999987
No 5
>3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E*
Probab=99.56 E-value=1.1e-15 Score=99.96 Aligned_cols=53 Identities=23% Similarity=0.227 Sum_probs=48.4
Q ss_pred cHHHHHHHHHHHHHHHhc-CCCceeeCCCCCChHHHHHHHHHcCCCCeEEEEecC
Q psy548 14 KRYERARVLGTRALQIAM-CAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLP 67 (84)
Q Consensus 14 trYelari~g~RArQL~~-GA~plV~~~~~~kp~~IAl~Ei~~gkI~~~i~R~~p 67 (84)
|||+|+.++++|||||+. |++|+|+.+ ++||++||++||++|+|.+.+....+
T Consensus 15 nRY~LV~~AAKRARQL~~~G~~plv~~~-~~Kpv~iALrEIa~GkV~~~~l~~~~ 68 (91)
T 3lu0_E 15 NRFDLVLVAARRARQMQVGGKDPLVPEE-NDKTTVIALREIEEGLINNQILDVRE 68 (91)
T ss_dssp SHHHHHHHHHHHHHHHHHTCCCSCCSSS-CCCSSCCSHHHHHSSSCEEESSSSCC
T ss_pred CHhHHHHHHHHHHHHHHhcCCCCccCCC-CCChHHHHHHHHHcCCCceeeCChhh
Confidence 899999999999999998 999999987 79999999999999999998765443
No 6
>2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.143.1.1 PDB: 1smy_E* 1zyr_E* 1iw7_E* 2a69_E* 2a6e_E 2a68_E* 2be5_E* 2cw0_E 3dxj_E* 2o5i_E 2o5j_E* 2ppb_E* 3aoh_E* 3aoi_E* 3eql_E* 1ynj_K* 1i6v_E* 1l9u_E 1l9z_E 1hqm_E* ...
Probab=99.49 E-value=3.3e-14 Score=93.90 Aligned_cols=48 Identities=23% Similarity=0.237 Sum_probs=42.2
Q ss_pred cHHHHHHHHHHHHHHHhcCC--CceeeC---CCCC---------ChHHHHHHHHHcCCCCeE
Q psy548 14 KRYERARVLGTRALQIAMCA--PVMVEL---EGET---------DPLQIAMKELKARKIPII 61 (84)
Q Consensus 14 trYelari~g~RArQL~~GA--~plV~~---~~~~---------kp~~IAl~Ei~~gkI~~~ 61 (84)
|||+||.++|+||+||+.|+ .|+++. ..+. ||++||++||++|+|.+.
T Consensus 15 nrY~LV~~aAKRARQI~~g~~k~~lv~~l~~~~~~~l~e~~~~~Kpv~iAL~EI~~Gki~~~ 76 (99)
T 2a6h_E 15 SKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG 76 (99)
T ss_dssp SHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE
T ss_pred CHhHHHHHHHHHHHHHHcCCccccchhhhhhcccccccccccCCCHHHHHHHHHHcCCeeec
Confidence 89999999999999999999 999872 1133 999999999999999864
No 7
>3hie_A Protein PSL1, exocyst complex component SEC3; PH domain, dimer, domain swapping, phosphate-binding, coiled coil, exocytosis; 2.00A {Saccharomyces cerevisiae}
Probab=57.23 E-value=8.1 Score=27.22 Aligned_cols=29 Identities=28% Similarity=0.475 Sum_probs=22.2
Q ss_pred CCCCeEEEEecCCCcEEE---eeccccceecC
Q psy548 56 RKIPIIIRRYLPDNSYED---WGIDELKIIDR 84 (84)
Q Consensus 56 gkI~~~i~R~~p~~~~e~---~~l~el~~~~~ 84 (84)
|.+.+--.|..+||+|.. |+|+||..||+
T Consensus 79 grV~lhK~K~N~ngsfsiGkTW~L~ELk~Ie~ 110 (171)
T 3hie_A 79 KLIQIHKARENSDGSFQIGRTWQLTELVRVEK 110 (171)
T ss_dssp TCEEEEEEEECTTSCEEEEEEEEGGGCCEEEE
T ss_pred ceEEEEEEEECCCCcEEeeeeeecccceeeec
Confidence 455566667788998765 99999998873
No 8
>3a58_A Exocyst complex component SEC3; protein complex, PH domain, GTPase, membrane traffic, coiled coil, exocytosis, phosphoprotein; HET: GNP; 2.60A {Saccharomyces cerevisiae}
Probab=36.00 E-value=18 Score=27.96 Aligned_cols=28 Identities=29% Similarity=0.459 Sum_probs=21.1
Q ss_pred CCCCeEEEEecCCCcEEE---eeccccceec
Q psy548 56 RKIPIIIRRYLPDNSYED---WGIDELKIID 83 (84)
Q Consensus 56 gkI~~~i~R~~p~~~~e~---~~l~el~~~~ 83 (84)
|.+.+--.|...||.|.. |.|+||..||
T Consensus 149 GRV~LhKaKeN~ngsFsIGKTW~L~ELk~Id 179 (320)
T 3a58_A 149 KLIQIHKARENSDGSFQIGRTWQLTELVRVE 179 (320)
T ss_dssp TCEEEEEEEECGGGCEEEEEEEEGGGCCEEE
T ss_pred ceEEEEEEEecCCCceEecceechhhhhhhh
Confidence 445555566777888765 9999999887
No 9
>2kxh_B Peptide of FAR upstream element-binding protein 1; RRM, FIR, FBP, protein-protein complex, protein binding; NMR {Homo sapiens}
Probab=29.85 E-value=26 Score=18.38 Aligned_cols=9 Identities=56% Similarity=0.313 Sum_probs=6.9
Q ss_pred HHHHHHHHh
Q psy548 22 LGTRALQIA 30 (84)
Q Consensus 22 ~g~RArQL~ 30 (84)
+-.|||||+
T Consensus 13 A~~RaRQIa 21 (31)
T 2kxh_B 13 ALQRARQIA 21 (31)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 347999995
No 10
>2npt_A Dual specificity mitogen-activated protein kinase; MAP2K5, MEK5, MKK PRKMK5, MAP kinase kinase 5, PHOX, PHOX-domain; 1.75A {Homo sapiens} SCOP: d.15.2.2 PDB: 2o2v_A 1wi0_A
Probab=29.06 E-value=45 Score=21.82 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=18.2
Q ss_pred CCeEEEEecCCCcEEEeecc
Q psy548 58 IPIIIRRYLPDNSYEDWGID 77 (84)
Q Consensus 58 I~~~i~R~~p~~~~e~~~l~ 77 (84)
-++.||=+.|||.-.||+++
T Consensus 13 ~~lVIRIk~p~~g~vDwaV~ 32 (106)
T 2npt_A 13 QVLVIRIKIPNSGAVDWTVH 32 (106)
T ss_dssp CCEEEEEEETTTEEEEEEEC
T ss_pred CceEEEEECCCCCccccccC
Confidence 47889999999999999997
No 11
>1jb0_D Photosystem 1 reaction centre subunit II; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.187.1.1 PDB: 3pcq_D*
Probab=24.76 E-value=69 Score=21.87 Aligned_cols=26 Identities=31% Similarity=0.336 Sum_probs=19.9
Q ss_pred HHcCCC-CeEEEEecCCCcEEEeeccc
Q psy548 53 LKARKI-PIIIRRYLPDNSYEDWGIDE 78 (84)
Q Consensus 53 i~~gkI-~~~i~R~~p~~~~e~~~l~e 78 (84)
|..=|| .+.|-|.+|||..+-+-.++
T Consensus 72 LrtfKI~dykiYRifP~Ge~~~LhPkD 98 (138)
T 1jb0_D 72 LRPRKINDYKIYRIFPDGETVLIHPKD 98 (138)
T ss_dssp TGGGTCCCCEEEEECTTCCEEEEETTT
T ss_pred eeeeecccceEEEEcCCCceEEecCCC
Confidence 444456 68999999999998876554
Done!